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Genome polyprotein [Cleaved into: P1 proteinase (EC 3.4.-.-) (N-terminal protein); Helper component proteinase (HC-pro) (EC 3.4.22.45); Protein P3; 6 kDa protein 1 (6K1); Cytoplasmic inclusion protein (CI) (EC 3.6.4.-); 6 kDa protein 2 (6K2); Viral genome-linked protein (VPg); Nuclear inclusion protein A (NI-a) (NIa) (EC 3.4.22.44) (49 kDa proteinase) (49 kDa-Pro) (NIa-pro); Nuclear inclusion protein B (NI-b) (NIb) (EC 2.7.7.48) (RNA-directed RNA polymerase); Capsid protein (CP) (Coat protein)]

 POLG_PSBMV              Reviewed;        3206 AA.
P29152;
01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
01-DEC-1992, sequence version 1.
10-OCT-2018, entry version 137.
RecName: Full=Genome polyprotein;
Contains:
RecName: Full=P1 proteinase;
EC=3.4.-.-;
AltName: Full=N-terminal protein;
Contains:
RecName: Full=Helper component proteinase;
Short=HC-pro;
EC=3.4.22.45;
Contains:
RecName: Full=Protein P3;
Contains:
RecName: Full=6 kDa protein 1;
Short=6K1;
Contains:
RecName: Full=Cytoplasmic inclusion protein;
Short=CI;
EC=3.6.4.-;
Contains:
RecName: Full=6 kDa protein 2;
Short=6K2;
Contains:
RecName: Full=Viral genome-linked protein;
AltName: Full=VPg;
Contains:
RecName: Full=Nuclear inclusion protein A;
Short=NI-a;
Short=NIa;
EC=3.4.22.44;
AltName: Full=49 kDa proteinase;
Short=49 kDa-Pro;
AltName: Full=NIa-pro;
Contains:
RecName: Full=Nuclear inclusion protein B;
Short=NI-b;
Short=NIb;
EC=2.7.7.48;
AltName: Full=RNA-directed RNA polymerase;
Contains:
RecName: Full=Capsid protein;
Short=CP;
AltName: Full=Coat protein;
Pea seed-borne mosaic virus (strain DPD1).
Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage;
Potyviridae; Potyvirus.
NCBI_TaxID=31736;
NCBI_TaxID=3888; Pisum sativum (Garden pea).
[1]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=1940858; DOI=10.1099/0022-1317-72-11-2625;
Johansen E., Rasmussen O.F., Heide M., Borkhardt B.;
"The complete nucleotide sequence of pea seed-borne mosaic virus
RNA.";
J. Gen. Virol. 72:2625-2632(1991).
[2]
REVIEW.
PubMed=11226583; DOI=10.1016/S0168-1702(01)00220-9;
Urcuqui-Inchima S., Haenni A.L., Bernardi F.;
"Potyvirus proteins: a wealth of functions.";
Virus Res. 74:157-175(2001).
-!- FUNCTION: Capsid protein: involved in aphid transmission, cell-to-
cell and systemis movement, encapsidation of the viral RNA and in
the regulation of viral RNA amplification.
-!- FUNCTION: Nuclear inclusion protein B: an RNA-dependent RNA
polymerase that plays an essential role in the virus replication.
-!- FUNCTION: Helper component proteinase: required for aphid
transmission and also has proteolytic activity. Only cleaves a
Gly-Gly dipeptide at its own C-terminus. Interacts with virions
and aphid stylets. Acts as a suppressor of RNA-mediated gene
silencing, also known as post-transcriptional gene silencing
(PTGS), a mechanism of plant viral defense that limits the
accumulation of viral RNAs. May have RNA-binding activity (By
similarity). {ECO:0000250}.
-!- FUNCTION: Cytoplasmic inclusion protein: has helicase activity. It
may be involved in replication.
-!- FUNCTION: Both 6K peptides are indispensable for virus
replication. {ECO:0000250}.
-!- FUNCTION: Nuclear inclusion protein A: has RNA-binding and
proteolytic activities.
-!- CATALYTIC ACTIVITY: Hydrolyzes glutaminyl bonds, and activity is
further restricted by preferences for the amino acids in P6 - P1'
that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-
Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The
natural substrate is the viral polyprotein, but other proteins and
oligopeptides containing the appropriate consensus sequence are
also cleaved.
-!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
+ RNA(n+1). {ECO:0000255|PROSITE-ProRule:PRU00539}.
-!- CATALYTIC ACTIVITY: Hydrolyzes a Gly-|-Gly bond at its own C-
terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the
processing of the potyviral polyprotein.
-!- SUBCELLULAR LOCATION: Capsid protein: Virion {ECO:0000305}.
-!- ALTERNATIVE PRODUCTS:
Event=Ribosomal frameshifting; Named isoforms=2;
Name=Genome polyprotein;
IsoId=P29152-1; Sequence=Displayed;
Note=Produced by conventional translation.;
Name=P3N-PIPO polyprotein;
IsoId=P0CJ99-1; Sequence=External;
Note=Produced by -1 ribosomal frameshifting in P3 ORF.;
-!- DOMAIN: The N-terminus of helper component proteinase is involved
in interaction with stylets. The central part is involved in
interaction with virions and the C-terminus is involved in cell-to
cell movement of the virus.
-!- PTM: VPg is uridylylated by the polymerase and is covalently
attached to the 5'-end of the genomic RNA. This uridylylated form
acts as a nucleotide-peptide primer for the polymerase (By
similarity). {ECO:0000250}.
-!- PTM: Potyviral RNA is expressed as two polyproteins which undergo
post-translational proteolytic processing. Genome polyprotein is
processed by NIa-pro, P1 and HC-pro proteinases resulting in the
production of at least ten individual proteins. P3N-PIPO
polyprotein is cleaved by P1 and HC-pro proteinases resulting in
the production of three individual proteins. The P1 proteinase and
the HC-pro cleave only their respective C-termini
autocatalytically. 6K1 is essential for proper proteolytic
separation of P3 from CI (By similarity). {ECO:0000250}.
-!- SIMILARITY: Belongs to the potyviridae genome polyprotein family.
{ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution (CC BY 4.0) License
-----------------------------------------------------------------------
EMBL; D10930; BAA01726.1; -; mRNA.
PIR; JQ1331; GNVSPV.
RefSeq; NP_056765.1; NC_001671.1.
ProteinModelPortal; P29152; -.
MEROPS; C04.010; -.
PRIDE; P29152; -.
GeneID; 1494045; -.
KEGG; vg:1494045; -.
OrthoDB; VOG0900003L; -.
Proteomes; UP000006689; Genome.
GO; GO:0019029; C:helical viral capsid; IEA:UniProtKB-KW.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0008026; F:ATP-dependent helicase activity; IEA:InterPro.
GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
GO; GO:0003723; F:RNA binding; IEA:InterPro.
GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
GO; GO:0018144; P:RNA-protein covalent cross-linking; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
InterPro; IPR011492; DEAD_Flavivir.
InterPro; IPR001456; HC-pro.
InterPro; IPR031159; HC_PRO_CPD_dom.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR002540; Pept_S30_P1_potyvir.
InterPro; IPR009003; Peptidase_S1_PA.
InterPro; IPR001592; Poty_coat.
InterPro; IPR001730; Potyv_NIa-pro_dom.
InterPro; IPR039560; Potyvirid-P3.
InterPro; IPR013648; PP_Potyviridae.
InterPro; IPR001205; RNA-dir_pol_C.
InterPro; IPR007094; RNA-dir_pol_PSvirus.
Pfam; PF07652; Flavi_DEAD; 1.
Pfam; PF00271; Helicase_C; 1.
Pfam; PF00863; Peptidase_C4; 1.
Pfam; PF00851; Peptidase_C6; 1.
Pfam; PF01577; Peptidase_S30; 1.
Pfam; PF00767; Poty_coat; 1.
Pfam; PF08440; Poty_PP; 1.
Pfam; PF13608; Potyvirid-P3; 1.
Pfam; PF00680; RdRP_1; 1.
PRINTS; PR00966; NIAPOTYPTASE.
SMART; SM00487; DEXDc; 1.
SMART; SM00490; HELICc; 1.
SUPFAM; SSF50494; SSF50494; 1.
SUPFAM; SSF52540; SSF52540; 2.
PROSITE; PS51744; HC_PRO_CPD; 1.
PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PROSITE; PS51194; HELICASE_CTER; 1.
PROSITE; PS51436; POTYVIRUS_NIA_PRO; 1.
PROSITE; PS51871; PV_P1_PRO; 1.
PROSITE; PS50507; RDRP_SSRNA_POS; 1.
2: Evidence at transcript level;
ATP-binding; Capsid protein; Complete proteome;
Covalent protein-RNA linkage; Helical capsid protein; Helicase;
Hydrolase; Nucleotide-binding; Nucleotidyltransferase; Phosphoprotein;
Protease; Ribosomal frameshifting; RNA-directed RNA polymerase;
Serine protease; Suppressor of RNA silencing; Thiol protease;
Transferase; Viral RNA replication; Virion.
CHAIN 1 3206 Genome polyprotein.
/FTId=PRO_0000420013.
CHAIN 1 397 P1 proteinase. {ECO:0000255}.
/FTId=PRO_0000040375.
CHAIN 398 856 Helper component proteinase.
{ECO:0000255}.
/FTId=PRO_0000040376.
CHAIN 857 1214 Protein P3. {ECO:0000250}.
/FTId=PRO_0000040377.
CHAIN 1215 1266 6 kDa protein 1. {ECO:0000250}.
/FTId=PRO_0000040378.
CHAIN 1267 1902 Cytoplasmic inclusion protein.
{ECO:0000250}.
/FTId=PRO_0000040379.
CHAIN 1903 1955 6 kDa protein 2. {ECO:0000250}.
/FTId=PRO_0000040380.
CHAIN 1956 2149 Viral genome-linked protein.
{ECO:0000250}.
/FTId=PRO_0000040381.
CHAIN 2150 2395 Nuclear inclusion protein A.
{ECO:0000250}.
/FTId=PRO_0000040382.
CHAIN 2396 2915 Nuclear inclusion protein B.
{ECO:0000250}.
/FTId=PRO_0000040383.
CHAIN 2916 3206 Capsid protein. {ECO:0000250}.
/FTId=PRO_0000040384.
DOMAIN 255 397 Peptidase S30. {ECO:0000255|PROSITE-
ProRule:PRU01219}.
DOMAIN 734 856 Peptidase C6. {ECO:0000255|PROSITE-
ProRule:PRU01080}.
DOMAIN 1338 1490 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 1494 1668 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
DOMAIN 2150 2368 Peptidase C4. {ECO:0000255|PROSITE-
ProRule:PRU00766}.
DOMAIN 2637 2761 RdRp catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00539}.
NP_BIND 1351 1358 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 450 453 Involved in interaction with stylet and
aphid transmission. {ECO:0000250}.
MOTIF 708 710 Involved in virions binding and aphid
transmission. {ECO:0000250}.
MOTIF 1440 1443 DECH box.
MOTIF 1994 2001 Nuclear localization signal.
{ECO:0000255}.
ACT_SITE 307 307 For P1 proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01219}.
ACT_SITE 316 316 For P1 proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01219}.
ACT_SITE 348 348 For P1 proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01219}.
ACT_SITE 742 742 For helper component proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
ACT_SITE 815 815 For helper component proteinase activity.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
ACT_SITE 2195 2195 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
ACT_SITE 2230 2230 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
ACT_SITE 2300 2300 For nuclear inclusion protein A activity.
{ECO:0000255|PROSITE-ProRule:PRU00766}.
SITE 397 398 Cleavage; by P1 proteinase.
{ECO:0000255|PROSITE-ProRule:PRU01219}.
SITE 856 857 Cleavage; by autolysis.
{ECO:0000255|PROSITE-ProRule:PRU01080}.
SITE 1214 1215 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 1266 1267 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 1902 1903 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 1955 1956 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2149 2150 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2395 2396 Cleavage; by NIa-pro. {ECO:0000250}.
SITE 2915 2916 Cleavage; by NIa-pro. {ECO:0000250}.
MOD_RES 2016 2016 O-(5'-phospho-RNA)-tyrosine.
{ECO:0000250}.
SEQUENCE 3206 AA; 364276 MW; 42A3D921BE9A0CBF CRC64;
MSTLVCQAVA APVWSNGART RRIRDADGEY RCTQCDMGFD SMTMARPVNH CCDGIMIDEY
NLYDDDPIMH LVDSKTPIKR GSQETEGDGM AAEAIKVTGA EPVNCFMVGT IKCKINENSI
VAKGVMAAIP RQLTQDEVFM RKARLQAAVA KSTIEREEKE RQFAFSKLEE KLRARREKLK
DGIVIKTRKG LEWREATPNQ QRGKLQSTSF DASGGKTLTP HTIYCKTKSS KFSNGGVKCA
TSKKMRTVRK PQSLKMKTES IDVLIEQVMT IAGKHAKQVT LIDKQKTNRV WIRRVNGVRL
LQVETKHHKG IISQKDASLN NLTKRVARHF ARKTAYIHPS DSITHGHSGV VFLRANISGS
KSYSIDDLFV VRGKRNGKLM ESRNKVAWRK MFQIDHFSIV GIKIWNAFDA EYVKLRDESV
SDHDCVGGIT PEECGILAAQ ILRVFYPCWR ITCTKCISNW LSKPTSEQIE HIYERGNLAI
QDLNKRIPSA HHVTQMVELL RQRIKNTTFD MGNNTKVHEL IGHRQDGVFR HLNRLNNSIL
AANGSSTIEW ESMNESLLEL ARWHNKRTES IASGGISSFR NKISAKAQIN FALMCDNQLD
TNGNFVWGER GYHAKRFFSE FFTKIDPKDG YSHHTVRATP TGVRHLAIGN LIIPGDLQKL
REKLEGVSIT AVGISEKCVS RRNGDFVYPC SCVTSENGKP VLSDVILPTR NHLVIGNTGD
PKLVDLPKTE TGRMWIAKEG YCYINIFFAM LVNVSEKDAK DFTKFVRDEI MPQLGKWPTM
MDVATACYKL AIIYPDVRDA QLPRILVDHS EQIFHVIDSY GSMTTGYHIL KAGTVSQLIS
FAHGALLGEM KMYRVGGTQK MEINMCCCQR KNLLIKQLIR AIYRPKLLTE IIETEPFVLM
LAIVSPSILK AMFRSGTFNQ AIKFYMHRSK PTAQTLAFLE ALSERVSRSR VLSEQFNIID
GALKELKSLA NMSMRTQHTY PIVQNQLDIM IERVSADAEL LRDGFVVSKG RVQALIEKNY
QDDLRNSFTD LPYVQQLQQT MSFSRVKHGF GELCESKDLS FSKEAWMGHL SSFSAGGKQI
IRLARTKSQQ MLASGGRRVT LAARNITMRM VTATFSEIMK FVNMLLVLSM IFKLWKQANT
LLEEREKDKW EKFDRSQNEL RRQLRYTLWR FEAQEGRQVT REEFFDYLKY NEGIENRHEL
INELIANQPL FSIQAKKHGE IRFEQTVALM ALLAMMFGSD RSDAVFSTLS KVRTIFTTMA
QEVRCQSIDD IHDVFDEKKA TIDFELATDQ PAQVQMDKTF CEWWQNQMEQ NRTVPHYRTG
GKFIEFTRSN AASVANEIAH TPDFSEYLIR GAVGSGKSTG LPCYLSAKGR VLLLEPTRPL
TENVCAQLRG SPFHKSPSMS MRNGHTFGST PIHVMTTGYA LHFFCNNVER IREYDFVIFD
ECHVIDSSAM SFYCALKEYS YQGKILKVSA TPPGREVEFK TQFPVTIATE DSLSFDQFVQ
AQGSGANCDI LKKGHNILVY VSSYNEVDRL SKLLVDRGFK VTKVDGRTMK LGGVEINTSG
TAEKPHFIVA TNIIENGVTL DIDVVVDFGV KVVAELDADA RTMRYNKQAI SYGERIQRLG
RVGRLKDGHA LRIGHTEKGI TEIPVAIAVE SAFQCFAYGL PVMTSNVSTS IIGNCTVKQA
RTMMNFELSP FFTVELVKYN GTMHPEIHKI LVPYKLRDSS MQLCKEAIPN SGVSRWHTAH
EYISHGIVLE TLKSDVRIPF YLKGVPEKVY EKIWNAVCVF KSDSGFGRMS TASACNVAYT
LKTDPLSITR TIAHIDALLI EEQEKKSQFD LMSSHVTNSS SISLAGLVNR LRSKWMVDHS
GENIVKLQNA RSQLLEFRGM DINLDDVESF RKFGCAETVR CQSKSEVSKT LQLKGKWNKP
LITSDFFVVC MVSIGCVVLM YQIFMAKWNE PVKLEGKSKA KTLRFRQARD NNAKYEVFAD
EDTKRHYFGE AYTKKGKKSG KARGMGVKTK KFVNVYGFDP CEYSLVRFVD PLTGLTYDRH
PMEHMMDVQE TIGDDRREAM WNDELDKQLF VTRPTIEAYY IKDKTTPALK IDLNPHNPMR
VCDKAETIAG FPEREFELRQ SGSATLVPYS EVPVQNEKQE FDEEHVRTEA ASLHFGLRDY
NPIAQAVCRI TNTGVDYDRS IFGIGFGQFL ITNAHCFKLN EGETRIVSRH GQFTIEKTHS
LPIHQVKDKD MVIVRLPKDF PPFPQRLQFR APQEREKICL VGSNFQEKSI QSVITESCMT
FKHNGGKYWK HWITTKEGHC GLPAVALKDG HIVGIHNLGG ENTNINYFTP FDADILDKYL
LNAEALQWTK GWKYNKNKVC WGGLELLDDN EPEESGLFRM VKLLKSLEED GVRTQSRDDA
WLEKEIKGSL KVVARCPGQL VTKHVVKGPC AMFQLYLELH EDAKSFFTPR MGSYGKSRLS
KGAFIKDIMK YSSNTVVGNV DCDVFENAID NVEKILWKAG MMQCEYVTDA EAIFQSLNMN
AAVGAMYQGK KKDYFEDFTA ADRELIVKQS CERLFLGKKG VWNGSLKAEL RPIEKVHENK
TRTFTAAPLD TLLGGKVCVD DFNNFFYSCH LRGPWTVGIT KFYAGWNEFL SKLPDGWLYC
DADGSRFDSS LTPYLINAVL ELRLRFMEEW DAGEQMLKNL YTEIIYTPIA TPDGSVIKKT
KGNNSGQPST VVDNTLMVIL AMQYSLQLLG VDFETQDEVV RYFANGDDLL IAVRPDCEFV
LKGLEIHFSN LGLNYNFSAR HHDKKDVWFM STRGILRDGI LIPKLEEERI VAILEWDRSR
EFSHRLDAIC AAMIEAWGYD ELLQHIRKFY YWLLEQEPYR SIAQEGKAPY IAETALRHLY
TNAMATQSEL EKYTEAINQH YNDEGGDGSI KVRLQAGDET KDDERRRKEE EDRKKREESI
DASQFGSNRD NKKNKNKESD TPNKLIVKSD RDVDAGSSGT ITVPRLEKIS AKIRMPKHKG
GVAISLQHLV DYNPAQVDIS NTRATQSQFD NWWRAVSQEY GVGDNEMQVL ASGLMVWCIE
NGTSPNINGM WTMMDGEEQV EYPLKPVMDN ARPTFRQIMA HFSDVAEAYI EKRNSTEVYI
PRYALQRNLR DPSLARYGFD FYEITAKTPV RAREAHFQMK AAAIRGKSNS LFGLDGNVGT
QEENTERHTA EDVNQNMHNL LGMRAM


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